In Blender 2.49 the win width and height were been calculated including an extra pixel (e.g. a fullscreen editor would be (width + 1) by (height + 1) )
In opposite to that, Blender 2.5 window/editor code were fixed to have the exact width,height size.
So although the BGE canvas code was still the same as 2.49 it was producing a wrong result.

I'm also adding some commentaries in the setViewport code. BGE is setting the viewports 1 pixel larger.
the setViewport command is been used as if one should pass (minx, miny, width, height), while it should be (minx, miny, maxx, maxy). I will take care of that later, if any one has extra comments on that, please let me know.